thank you.. I had to repeat 12 hours of aligment.. again!!
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sam file error
Hi, I was converting my sam file (after alignment with bowtie2) in bam format. I encountered the error:
[E::sam_parse1] invalid QUAL character
[W::sam_read1_sam] Parse error at line 11129453
command:
samtools view -S -b -o input.bam ../alignment/input.sam
Alignment works fine. This is the output:
22504890 reads; of these:
18951369 (84.21%) were paired; of these:
574151 (3.03%) aligned concordantly 0 times
13965369 (73.69%) aligned concordantly exactly 1 time
4411849 (23.28%) aligned concordantly >1 times
3553521 (15.79%) were unpaired; of these:
98535 (2.77%) aligned 0 times
2418010 (68.05%) aligned exactly 1 time
1036976 (29.18%) aligned >1 times
96.99% overall alignment rate
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I have no clue, with other fastq files is working fine
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I found the problem. After trimmomatic's trimming, I get paired and unpaired fastq files. I feed bowtie2 with both, paired files and unpaired with the option -U. The point Is that unpaired fastq file (file.R2.U.fastq) was very low quality. Removing unpaired files, the sam file was not corrupted and I was able to convert It into bam.
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